Course fee

Course content

Perl is the ideal programming language for biological data analysis. The course is for students with little or no prior knowledge in perl. Familiarity in using a Unix command line (e.g. Mac OSX or Linux) is a requirement for the course. It is aimed at students who need computational skills to handle large datasets. The course will follow the book “Learning Perl”. It will consist of lectures to introduce all topics and computer assignments to be completed individually after each lecture. The course will also include practical computational exercises.

To complete the course, students are expected to complete a short project, either from their own work or pre-defined.

Topics covered will include:

introduction to command line and writing perl scripts

handling scalar data, control structures

lists/arrays

subroutines

input/output

regular expressions and pattern matching

conditional operators

strings and sorting

loops

hashes

introduction to modules such as bioperl

By the end of the course, students should:

understand and be able to implement all fundamental elements of Perl programming

be able to write programs to perform common bioinformatics tasks

be able to understand and debug Perl programs

be competent using a Unix environment

Entry requirements

To get the maximum benefit from the course we would like you to

Be able to bring your own Mac or Linux laptop for the practical computational exercises. If you don’t have a Mac or Linux computer to bring please contact us at education@scilifelab.uu.se before you apply.

Be familiar in using the Unix command line (Mac OSX or Linux). We will not teach Unix in detail in the course and you will have considerable trouble to follow the practical computational exercises if you are not reasonably used to work in a Unix. Other course are available at SciLifeLab that introduce the basics in Unix.

It is strongly recommended that students read the course book “Learning Perl, 6th Edition” (Schwartz et al.) before attending the course.

Selection criteria

Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance.

Date and time

2017-09-11 - 2017-09-15

Location

Husargatan 3, Uppsala

SciLifeLab has been created by the coordinated effort of four universities in Stockholm and Uppsala: Stockholm University, Karolinska Institutet, KTH Royal Institute of Technology and Uppsala University.